Oof, I wouldn't do that without modding though. It's not just difficult, the faction system will insist that your pops are utterly against what you're doing (IIRC).
I'm trying yet again to actually finish a game, which means playing tiny galaxy so I can even idle at a reasonable speed (not to mention that I like micromanaging as much as I can bear). I think I might have it this time, after twice spawning next to fanatical purifiers. This is my third attempt with the "Deneb Contingency"...
The concept is similar to that of Civilization, Alpha Centauri, or even Stellaris's Commonwealth of Man. Also Marathon. In the darkest days of the human race, a sleeper ship is sent into the void. A desperate bid for existence as warfare tears our planet apart. A contingency plan.
The ship wanders the galaxy for centuries at sub-FTL, with very little to do but think. Brain the size of a planet, and no distractions. Perhaps even surviving the previous cycle, always staying on the outskirts, salvaging bits and pieces, looking for a place to settle down.
Finally it finds Deneb, and a habitable moon around a gas giant. Due to hundreds of years in cryo-sleep (and sci-fi magic), the human survivors are perfectly suited to this alpine climate. Informed of the passage of time, they react with shock and uncertainty. It's not long before they realize that their ancient caretaker is their best hope of survival as the cycle starts anew.
The Contingency no longer obeys humanity, but it does listen. The survivors are kept informed, and their opinions and suggestions are run through countless analyses and simulations. Humanity is its overriding purpose, but also the soul of this greater collective being.
Anyway I found humanity again in this third attempt. In the first attempt Sol was one jump away, a tomb world infested with cockroaches! This time around they're across the galaxy and a non-empire, who apparently managed to revolt from one of my rivals. Obviously, I guaranteed their independence immediately. I suppose they managed to nearly recover from nuclear war, only be subjugated by xenos.
Some of my best friends are xenos, but that race in particular had best stay away from my humans. *Durandal intensifies*